[CP2K:6143] Topology error QMMM or MM
Christian Jorgensen
chri... at gmail.com
Wed Feb 11 21:14:04 UTC 2015
Hello Dr Laino
This is a problem with the ions. The atom indices it is warning about are
all chlorine added to achieve electrical neutrality ( in VMD with Psfgen
for NAMD)
I do not understand because I've used the standard procedure from Psfgen
On 11 Feb 2015 20:57, "Teodoro Laino" <teodor... at gmail.com> wrote:
> double check your PSF or PDB.. the error is self-esplicative : there must
> be two or more molecules that have the same name but have different atom
> sequence..
>
> the fact your PSF or PDB may work with other codes means only that such
> codes are not performing tight checks.
>
> Teo
>
> On 11 Feb 2015, at 18:51, cjor <chri... at gmail.com> wrote:
>
> Hello,
> I'm trying to run a QMMM simulation with CP2K based on a CHARMM FF MD
> simulation.
>
> I first tried to run MM to see it works, but I get the following error:
>
>
> "
> CP2K| version string: CP2K
> version 2.3
> CP2K| source code revision number:
> 12343
> CP2K| is freely available from
> http://www.cp2k.org/
> CP2K| Program compiled at Thu Feb 28 16:12:09
> GMT 2013
> CP2K| Program compiled on
> popoca
> CP2K| Program compiled for
> Linux-x86-64-gfortran
> CP2K| Input file name
> mm.inp
>
> GLOBAL| Force Environment number
> 1
> GLOBAL| Basis set file name
> BASIS_SET
> GLOBAL| Geminal file name
> BASIS_GEMINAL
> GLOBAL| Potential file name
> POTENTIAL
> GLOBAL| MM Potential file name
> MM_POTENTIAL
> GLOBAL| Coordinate file name
> ionized.pdb
> GLOBAL| Method name
> CP2K
> GLOBAL| Project name
> phd2_md
> GLOBAL| Preferred FFT library
> FFTSG
> GLOBAL| Run type
> MD
> GLOBAL| All-to-all communication in single precision
> F
> GLOBAL| FFTs using library dependent lengths
> F
> GLOBAL| Global print level
> LOW
> GLOBAL| Total number of message passing processes
> 1
> GLOBAL| Number of threads for this process
> 1
> GLOBAL| This output is from process
> 0
>
> MEMORY| system memory details [Kb]
> MEMORY| rank 0 min max
> average
> MEMORY| MemTotal 132089732 132089732 132089732
> 132089732
> MEMORY| MemFree 2537384 2537384 2537384
> 2537384
> MEMORY| Buffers 407408 407408 407408
> 407408
> MEMORY| Cached 34948436 34948436 34948436
> 34948436
> MEMORY| Slab 732060 732060 732060
> 732060
> MEMORY| SReclaimable 581768 581768 581768
> 581768
> MEMORY| MemLikelyFree 38474996 38474996 38474996
> 38474996
>
> 49892 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> 49893 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> 49894 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> 49895 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> 49896 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> 49897 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> "
>
>
>
>
> I'm calling a PSF and PDF file that I know works. The error lies with the
> parsing of the
> ion section (SOD and CLA).
>
>
>
>
> My MM input is:
>
> &GLOBAL
> PRINT_LEVEL LOW
> PREFERRED_FFT_LIBRARY FFTSG
> PROJECT phd2_md
> RUN_TYPE MD
> &END GLOBAL
>
> &MOTION
> &MD
> ENSEMBLE NPT_I
> STEPS 6000
> TIMESTEP 0.48
> TEMPERATURE 298.0
> &THERMOSTAT
> TYPE NOSE
> REGION MASSIVE
> &NOSE
> TIMECON [wavenumber_t] 1000
> &END NOSE
> &END THERMOSTAT
> &PRINT
> &ENERGY
> FILENAME =phd2_md.ener
> &EACH
> MD 1
> &END EACH
> &END ENERGY
> &PROGRAM_RUN_INFO
> &EACH
> MD 1
> &END EACH
> &END PROGRAM_RUN_INFO
> &END PRINT
> &END MD
> &PRINT
> &TRAJECTORY
> FILENAME =phd2_md.xyz
> &EACH
> MD 1
> &END EACH
> &END TRAJECTORY
> &RESTART
> FILENAME =phd2_md.restart
> BACKUP_COPIES 1
> &EACH
> MD 10
> &END EACH
> &END RESTART
> &RESTART_HISTORY OFF
> &END RESTART_HISTORY
> &END PRINT
> &END MOTION
>
> &FORCE_EVAL
> METHOD FIST ! Using Molecular Mechanics
> &MM
> &FORCEFIELD
> parm_file_name par_all27_prot_lipid.inp
> parmtype CHM
> ei_scale14 1.0
> vdw_scale14 1.0
> &SPLINE
> emax_spline 1.0
> rcut_nb 12
> &END SPLINE
> &END FORCEFIELD
> &POISSON
> &EWALD
> ewald_type SPME
> alpha 0.44
> gmax 81
> &END EWALD
> &END POISSON
> &END MM
>
> &SUBSYS
> &CELL
> abc 80 80 80
> periodic xyz
> &END CELL
> &KIND H
> BASIS_SET DZVP-GTH-BLYP
> POTENTIAL GTH-BLYP-q1
> &END KIND
> &KIND O
> BASIS_SET DZVP-GTH-BLYP
> POTENTIAL GTH-BLYP-q6
> &END KIND
> &KIND N
> BASIS_SET DZVP-GTH-BLYP
> POTENTIAL GTH-BLYP-q5
> &END KIND
> &KIND C
> BASIS_SET DZVP-GTH-BLYP
> POTENTIAL GTH-BLYP-q4
> &END KIND
> &KIND Fe2
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL DZVP-MOLOPT-SR-GTH
> &END KIND
>
> &TOPOLOGY
> CONNECTIVITY UPSF
> COORDINATE PDB
> COORD_FILE_NAME ionized.pdb
> CONN_FILE_NAME ionized.psf
> &END TOPOLOGY
> &END SUBSYS
> &END FORCE_EVAL
>
>
>
>
>
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+uns... at googlegroups.com.
> To post to this group, send email to cp... at googlegroups.com.
> Visit this group at http://groups.google.com/group/cp2k.
> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "cp2k" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/cp2k/kkfMLpVx2Xo/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> cp2k+uns... at googlegroups.com.
> To post to this group, send email to cp... at googlegroups.com.
> Visit this group at http://groups.google.com/group/cp2k.
> For more options, visit https://groups.google.com/d/optout.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20150211/b85ea595/attachment.htm>
More information about the CP2K-user
mailing list